One piece of advice, I would ensure QA tests include checks to make sure that the skip function works. When the ggplot package was updated, the update broke the Getting and Cleaning data module, the ggplot units. The questions were not answerable and the skip function didn't work either.
You are the reason I was able to pass the R programming unit, John Hopkins Coursera. Thank you sooooo much.
I highly recommend using swirl if you're just getting into R.
The more I use R the less I use of base and mostly use the Hadley Wickham Universe of dplyr, tidyr, ggplot/ggvis etc.. This teaches mostly base and not the functional programming parts (Boy do I HATE loops and R base has a great list system that people seem to ignore)
The paper's examples might be slightly dated as they use dplyr's predecessor, plyr. I imagine they're pretty similar though.